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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DENSE Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
cont_img = 'lopesi2bc/denovogenes'
genEra_img = 'josuebarrera/genera'
genEra_fast_img = 'lopesi2bc/genera_fast'
plugins {
id 'nf-validation@0.3.1'
}
// Global default params, used in configs
params {
// Input options
gendir = null
outdir = 'dense_results'
focal = null
strategy = 1
tree = null
help = false
trgs = null
genera_out = null
genera_db = null
genera_fast = false
taxids = null
taxdump = null
trg_node = null
trg_rank = 'genus'
synteny = true
synteny_window = 4
synteny_anchors = 1
num_outgroups = 1
orthodir = null
orthotool = 'diamond'
diamond_sens = null
trgsblastdir = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
config_profile_name = null
config_profile_description = null
}
// Load base.config by default for all pipelines
//includeConfig 'conf/base.config'
profiles {
test { includeConfig 'conf/test.config' }
// test_full { includeConfig 'conf/test_full.config' }
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
}
pbspro {
process {
executor = 'pbspro'
queueSize = 50
// if you want to change options here use 'clusterOptions'
withLabel: parallel_job {
clusterOptions = "-l walltime=43800:00:00 -l ncpus=${params.max_cpus}"
}
withName: GENERA {
clusterOptions = "-l walltime=43800:00:00 -l ncpus=${params.max_cpus} -l mem=${MemoryUnit.of(params.max_memory).toMega()}mb"
}
}
}
perso {
process {
executor = 'local'
queueSize = 30
// if you want to change options here use 'clusterOptions'
withLabel: parallel_job {
executor = 'pbspro'
clusterOptions = "-q bim -l walltime=43800:00:00 -l ncpus=${params.max_cpus} -l mem=75gb"
}
withName: GENERA {
executor = 'pbspro'
clusterOptions = "-q bim -l walltime=43800:00:00 -l ncpus=${params.max_cpus} -l mem=${MemoryUnit.of(params.max_memory).toMega()}mb"
}
}
}
perslow {
process {
executor = 'pbspro'
queueSize = 15
clusterOptions = "-q lowprio -l walltime=43800:00:00 -l ncpus=${params.max_cpus}"
withLabel: parallel_job {
executor = 'pbspro'
clusterOptions = "-q lowprio -l walltime=43800:00:00 -l ncpus=${params.max_cpus} -l mem=75gb"
}
withName: GENERA {
executor = 'pbspro'
clusterOptions = "-q lowprio -l walltime=43800:00:00 -l ncpus=${params.max_cpus} -l mem=${MemoryUnit.of(params.max_memory).toMega()}mb"
}
}
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
process{
container = cont_img
withName: GENERA {
container = genEra_img
}
withName: GENERA_FAST {
container = genEra_fast_img
}
}
docker{
enabled = true
userEmulation = true
cacheDir = "${projectDir}/containers"
}
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
process{
container = "docker://${cont_img}"
withName: GENERA {
container = "docker://${genEra_img}"
}
withName: GENERA_FAST {
container = "docker://${genEra_fast_img}"
}
}
singularity {
enabled = true
autoMounts = true
cacheDir = "${projectDir}/containers"
}
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
process{
container = "docker://${cont_img}"
withName: GENERA {
container = "docker://${genEra_img}"
}
withName: GENERA_FAST {
container = "docker://${genEra_fast_img}"
}
}
apptainer {
enabled = true
autoMounts = true
cacheDir = "${projectDir}/containers"
}
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = ''
docker.registry = ''
podman.registry = ''
singularity.registry = ''
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'DENSE'
author = """Paul Roginski"""
homePage = 'https://github.com/i2bc/dense.git'
description = """Identifies genes that have emerged de novo (from non-coding DNA)."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.3'
version = '1.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
// includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}